PB1699: GENOMIC AND TRANSCRIPTOMIC PROFILING REVEALS NOVEL GENE FUSIONS AND MARKERS OF CLINICAL RESPONSE IN PEDIATRIC ACUTE LYMPHOBLASTIC LEUKEMIA
Authors: Borbála Péterffy, Szilvia Krizsán, Bálint Egyed, Gábor Bedics, Anna Bekő, Dániel János Erdélyi, Judit Müller, Tibor Nagy, Lajos László Hegyi, Zsuzsanna Jakab, György Péter, Marianna Zombori, Krisztina Csanádi, Gábor Ottóffy, Katalin Csernus, Ágnes Vojcek, Lilla Györgyi Tiszlavicz, Krisztina Míta Gábor, Ágnes Kelemen, Péter Hauser, Krisztián Kállay, Gabriella Kertész, Zsuzsanna Gaál, István Szegedi, Ágnes Márk, Irén Haltrich, Zsuzsanna Hevessy, Anikó Ujfalusi, Béla Kajtár, Csongor Kiss, Gergely Kriván, András Matolcsy, Gábor Kovács, Csaba Bödör, Donát Alpár
Journal: HemaSphere (2023)

Topic: 1. Acute lymphoblastic leukemia - Biology & Translational Research Background: Advances in therapeutic strategies of pediatric acute lymphoblastic leukemia (ALL) improved 5-year survival rates; however, the clinical management of disease progression and relapse remains challenging. Profiling molecular markers with prognostic and/or predictive significance in individual patients is crucial for refined risk assessment and precise patient stratification, underlining the importance of comprehensive molecular characterization. Aims: To interrogate the genomic and transcriptomic landscape of Hungarian children diagnosed with ALL in order to identify alterations with prognostic and therapeutic relevance, and to facilitate a more advanced, risk-adapted therapy selection for clinical decision-making. Methods: Diagnostic bone marrow samples with a mean blast percentage of 78.4% were investigated from 180 patients diagnosed with B-ALL (n=150) or T-ALL (n=30). Additionally, samples drawn at the time of relapse were analyzed from 19 patients. Gene fusions were identified with the TruSight RNA Pan-Cancer Panel targeting 1,385 genes, while mutation screening was performed using a custom QIASeq Targeted DNA Panel covering 102 disease-relevant genes. Copy number alterations were screened with multiplex ligation-dependent probe amplification using SALSA P335, P202 and P383 probemixes. Measurable residual disease (MRD) monitoring was performed by flow cytometry. Results: Gene fusions were identified in 34.9% of B-ALL and 46.4% of T-ALL patients, with ETV6-RUNX1, STIL-TAL1, P2RY8-CRLF2 and TCF3-PBX1 being the most common alterations. Five novel fusions involving JAK2, PAX5, KMT2A and RUNX1 genes were also observed. Targeted mutation screening revealed a higher number of aberrations in T-ALL patients (B-ALL: 2.01±1.88 vs. T-ALL: 3.86±3.00; p<0.001). In B-ALL, variants most frequently affected RAS-pathway genes (KRAS 18.4%, NRAS 17.8% and FLT3 10.2%), while NOTCH1 (58.6%), PHF6 (27.5%), PTEN (17.2%) and WT1 (17.2%) were the most commonly altered genes in T-ALL. IKZF1 deletion was observed in 18.1% of B-ALL patients, with eight of them showing IKZF1plus genotype. The vast majority (75.0%) of UBA2 mutations accompanied ETV6-RUNX1 fusion. Besides all patients with BCR-ABL1 fusion harboring IKZF1 deletion, BCR-ABL1-like subtype showed significant association with IKZF1 deletions (p=0.028). NT5C2 mutations, undetectable at diagnosis were identified at relapse in three patients. All CCND3-mutant cases (n=9) were MRD-negative with flow cytometry at day 33 and only one patient had detectable blasts at day 78. NOTCH1 and WT1 mutation frequently co-occurred with MRD-positivity at days 33 and 78. Scrutiny of the dynamics of early therapy response from diagnosis to day 15 revealed a slower decrease of MRD in the presence of RUNX1 mutation with high variant allele frequency (‘high burden’, VAF≥25%; wild type vs. ‘high burden’ p=0.004). The dynamics of MRD decline from day 15 to day 78 differed in TP53-mutant patients: a slower response to therapy was observed in high burden cases (‘high burden’ vs. wild type, ‘high burden’ vs. ‘low burden’; p<0.001). Survival analysis showed significantly shorter 3-year overall and event-free survival in RUNX1 and/or TP53 ‘high burden’ patients (OS: 92.3% vs. 50.0%, p=0.0001; EFS: 87.0% vs. 50.0%, p=0.002). Summary/Conclusion: With novel gene fusions and uncovered associations between the dynamics of MRD decline, TP53 and RUNX1 high burden mutations in this real-world cohort, our dataset provides valuable, clinically relevant insights to the genomic and transcriptomic landscape of children diagnosed with ALL. Keywords: Pediatric, ALL, Prognosis, Mutation analysis